[2021-09-15 00:05:29,783] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-15 00:05:29,783] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-15 00:05:29,783] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-15 00:05:29,784] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-15 00:05:29,784] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-15 00:05:29,784] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJF5GDRXY/merged [2021-09-15 00:05:31,133] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-15 00:05:31,133] multiqc [INFO ] This is MultiQC v1.9 [2021-09-15 00:05:31,133] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJF5GDRXY/merged [2021-09-15 00:05:31,134] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJF5GDRXY/merged [2021-09-15 00:05:31,134] multiqc [INFO ] Template : default [2021-09-15 00:05:31,134] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-15 00:05:31,134] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJF5GDRXY/merged [2021-09-15 00:05:31,134] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2021-09-15 00:05:31,134] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9998619/tmpxrd2hbdq [2021-09-15 00:05:31,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK12_hic_fastqc.html [2021-09-15 00:05:31,254] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK12_hic_fastqc.html [2021-09-15 00:05:31,297] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK11_hic_fastqc.html [2021-09-15 00:05:31,299] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK11_hic_fastqc.html [2021-09-15 00:05:31,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK17_hic_fastqc.html [2021-09-15 00:05:31,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK17_hic_fastqc.html [2021-09-15 00:05:31,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:31,407] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-15 00:05:36,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK17_hic_fastqc.html [2021-09-15 00:05:36,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK17_hic_fastqc.html [2021-09-15 00:05:36,134] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK19_hic_fastqc.html [2021-09-15 00:05:36,135] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK19_hic_fastqc.html [2021-09-15 00:05:36,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK14_hic_fastqc.html [2021-09-15 00:05:36,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK14_hic_fastqc.html [2021-09-15 00:05:36,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK12_hic_fastqc.html [2021-09-15 00:05:36,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK12_hic_fastqc.html [2021-09-15 00:05:36,292] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK18_hic_fastqc.html [2021-09-15 00:05:36,294] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK18_hic_fastqc.html [2021-09-15 00:05:36,341] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK13_hic_fastqc.html [2021-09-15 00:05:36,343] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK13_hic_fastqc.html [2021-09-15 00:05:36,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_undetermined_fastqc.html [2021-09-15 00:05:36,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_undetermined_fastqc.html [2021-09-15 00:05:36,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK11_hic_fastqc.html [2021-09-15 00:05:36,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK11_hic_fastqc.html [2021-09-15 00:05:36,481] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_undetermined_fastqc.html [2021-09-15 00:05:36,483] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_undetermined_fastqc.html [2021-09-15 00:05:36,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK13_hic_fastqc.html [2021-09-15 00:05:36,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK13_hic_fastqc.html [2021-09-15 00:05:36,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK18_hic_fastqc.html [2021-09-15 00:05:36,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK18_hic_fastqc.html [2021-09-15 00:05:36,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK19_hic_fastqc.html [2021-09-15 00:05:36,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n01_JK19_hic_fastqc.html [2021-09-15 00:05:36,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK14_hic_fastqc.html [2021-09-15 00:05:36,708] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJF5GDRXY_n02_JK14_hic_fastqc.html [2021-09-15 00:05:37,110] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-15 00:05:37,112] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-15 00:05:37,120] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-15 00:05:37,130] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-15 00:05:37,134] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2021-09-15 00:05:37,139] multiqc [DEBUG ] No samples found: conpair [2021-09-15 00:05:37,144] multiqc [DEBUG ] No samples found: peddy [2021-09-15 00:05:37,148] multiqc [DEBUG ] No samples found: somalier [2021-09-15 00:05:37,153] multiqc [DEBUG ] No samples found: methylQA [2021-09-15 00:05:37,160] multiqc [DEBUG ] No samples found: mosdepth [2021-09-15 00:05:37,165] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-15 00:05:37,169] multiqc [DEBUG ] No samples found: qualimap [2021-09-15 00:05:37,173] multiqc [DEBUG ] No samples found: preseq [2021-09-15 00:05:37,178] multiqc [DEBUG ] No samples found: quast [2021-09-15 00:05:37,183] multiqc [DEBUG ] No samples found: qorts [2021-09-15 00:05:37,187] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-15 00:05:37,192] multiqc [DEBUG ] No samples found: rockhopper [2021-09-15 00:05:37,196] multiqc [DEBUG ] No samples found: rsem [2021-09-15 00:05:37,206] multiqc [DEBUG ] No samples found: rseqc [2021-09-15 00:05:37,211] multiqc [DEBUG ] No samples found: busco [2021-09-15 00:05:37,215] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-15 00:05:37,219] multiqc [DEBUG ] No samples found: disambiguate [2021-09-15 00:05:37,224] multiqc [DEBUG ] No samples found: supernova [2021-09-15 00:05:37,235] multiqc [DEBUG ] No samples found: deeptools [2021-09-15 00:05:37,240] multiqc [DEBUG ] No samples found: sargasso [2021-09-15 00:05:37,244] multiqc [DEBUG ] No samples found: verifybamid [2021-09-15 00:05:37,249] multiqc [DEBUG ] No samples found: mirtrace [2021-09-15 00:05:37,254] multiqc [DEBUG ] No samples found: happy [2021-09-15 00:05:37,258] multiqc [DEBUG ] No samples found: mirtop [2021-09-15 00:05:37,264] multiqc [DEBUG ] No samples found: homer [2021-09-15 00:05:37,269] multiqc [DEBUG ] No samples found: macs2 [2021-09-15 00:05:37,273] multiqc [DEBUG ] No samples found: theta2 [2021-09-15 00:05:37,278] multiqc [DEBUG ] No samples found: snpeff [2021-09-15 00:05:37,284] multiqc [DEBUG ] No samples found: gatk [2021-09-15 00:05:37,289] multiqc [DEBUG ] No samples found: htseq [2021-09-15 00:05:37,294] multiqc [DEBUG ] No samples found: bcftools [2021-09-15 00:05:37,298] multiqc [DEBUG ] No samples found: featureCounts [2021-09-15 00:05:37,304] multiqc [DEBUG ] No samples found: fgbio [2021-09-15 00:05:37,317] multiqc [DEBUG ] No samples found: dragen [2021-09-15 00:05:37,321] multiqc [DEBUG ] No samples found: dedup [2021-09-15 00:05:37,326] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-15 00:05:37,346] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-15 00:05:37,350] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-15 00:05:37,353] multiqc [DEBUG ] No samples found: picard [2021-09-15 00:05:37,357] multiqc [DEBUG ] No samples found: prokka [2021-09-15 00:05:37,362] multiqc [DEBUG ] No samples found: samblaster [2021-09-15 00:05:37,369] multiqc [DEBUG ] No samples found: samtools [2021-09-15 00:05:37,374] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-15 00:05:37,379] multiqc [DEBUG ] No samples found: bamtools [2021-09-15 00:05:37,383] multiqc [DEBUG ] No samples found: jellyfish [2021-09-15 00:05:37,390] multiqc [DEBUG ] No samples found: vcftools [2021-09-15 00:05:37,394] multiqc [DEBUG ] No samples found: longranger [2021-09-15 00:05:37,399] multiqc [DEBUG ] No samples found: stacks [2021-09-15 00:05:37,404] multiqc [DEBUG ] No samples found: varscan2 [2021-09-15 00:05:37,416] multiqc [DEBUG ] No samples found: bbmap [2021-09-15 00:05:37,420] multiqc [DEBUG ] No samples found: bismark [2021-09-15 00:05:37,425] multiqc [DEBUG ] No samples found: biscuit [2021-09-15 00:05:37,430] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-15 00:05:37,434] multiqc [DEBUG ] No samples found: hicup [2021-09-15 00:05:37,439] multiqc [DEBUG ] No samples found: hicpro [2021-09-15 00:05:37,444] multiqc [DEBUG ] No samples found: salmon [2021-09-15 00:05:37,448] multiqc [DEBUG ] No samples found: kallisto [2021-09-15 00:05:37,453] multiqc [DEBUG ] No samples found: slamdunk [2021-09-15 00:05:37,458] multiqc [DEBUG ] No samples found: star [2021-09-15 00:05:37,463] multiqc [DEBUG ] No samples found: hisat2 [2021-09-15 00:05:37,467] multiqc [DEBUG ] No samples found: tophat [2021-09-15 00:05:37,472] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-15 00:05:37,476] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-15 00:05:37,481] multiqc [DEBUG ] No samples found: snpsplit [2021-09-15 00:05:37,485] multiqc [DEBUG ] No samples found: kat [2021-09-15 00:05:37,489] multiqc [DEBUG ] No samples found: leehom [2021-09-15 00:05:37,494] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-15 00:05:37,498] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-15 00:05:37,502] multiqc [DEBUG ] No samples found: cutadapt [2021-09-15 00:05:37,507] multiqc [DEBUG ] No samples found: flexbar [2021-09-15 00:05:37,511] multiqc [DEBUG ] No samples found: kaiju [2021-09-15 00:05:37,516] multiqc [DEBUG ] No samples found: kraken [2021-09-15 00:05:37,520] multiqc [DEBUG ] No samples found: malt [2021-09-15 00:05:37,525] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-15 00:05:37,529] multiqc [DEBUG ] No samples found: sickle [2021-09-15 00:05:37,534] multiqc [DEBUG ] No samples found: skewer [2021-09-15 00:05:37,538] multiqc [DEBUG ] No samples found: sortmerna [2021-09-15 00:05:37,542] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-15 00:05:37,547] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-15 00:05:37,552] multiqc [DEBUG ] No samples found: afterqc [2021-09-15 00:05:37,556] multiqc [DEBUG ] No samples found: fastp [2021-09-15 00:05:38,344] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2021-09-15 00:05:38,565] multiqc [DEBUG ] No samples found: pycoqc [2021-09-15 00:05:38,570] multiqc [DEBUG ] No samples found: minionqc [2021-09-15 00:05:38,575] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-15 00:05:38,579] multiqc [DEBUG ] No samples found: clusterflow [2021-09-15 00:05:38,584] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-15 00:05:38,589] multiqc [DEBUG ] No samples found: interop [2021-09-15 00:05:38,594] multiqc [DEBUG ] No samples found: ivar [2021-09-15 00:05:38,598] multiqc [DEBUG ] No samples found: flash [2021-09-15 00:05:38,602] multiqc [DEBUG ] No samples found: seqyclean [2021-09-15 00:05:38,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-15 00:05:38,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-15 00:05:38,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-15 00:05:38,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-15 00:05:38,623] multiqc [INFO ] Compressing plot data [2021-09-15 00:05:38,906] multiqc [INFO ] Report : multiqc_report.html [2021-09-15 00:05:38,906] multiqc [INFO ] Data : multiqc_data [2021-09-15 00:05:38,906] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9998619/tmpxrd2hbdq/multiqc_data' to '/scratch/gencore/logs/html/HJF5GDRXY/merged/multiqc_data' [2021-09-15 00:05:39,073] multiqc [INFO ] MultiQC complete